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A checkpoint is a point in a video game in which progress is automatically saved, so that if the player character dies, they will respawn at this point. While most Metroid games require manual saving through Save Stations, more recent titles in the series have featured some checkpoints as well. Checkpoints are present in Metroid Prime 2: Echoes, Metroid Prime Hunters, Metroid Prime 3: Corruption and Metroid: Other M. They usually appear before some bosses or especially difficult points, such as the Tetra Vista, the final battles with Dark Samus, Rundas, the Mining cannon and the second phase of the Queen Metroid battle. In Corruption, if Samus dies during the battle with Aurora Unit 313 on Hypermode difficulty, she will be forced to restart the final battle from the conflict with Dark Samus herself. There is a catch with checkpoints, as they are not permanent. They last until the game is turned off, exited, or the player declines to continue the game on a Game Over screen, and then they will have to resume the game from the last used Save Station.

"You can restart your game from these spots as you progress. Checkpoints are not saved, so if you choose NO on the Continue Screen, exit the game or turn the power off, the next time you play the game, you will start from the last save point."